Telomere-to-telomere assembly of a fish Y chromosome reveals the origin of a young sex chromosome pair

Genome Biology

Meiying Wu¹  Tian Tian¹  Yu Gao²  Lingzhan Xue³  Dapeng Li⁴  Luohao Xu⁵  Haiping Fan⁶  Zhen Huang⁷  Yongji Huang⁸ 

[1] Aquaculture and Genetic Breeding Laboratory, Freshwater Fisheries Research Institute of Fujian, 350002, Fuzhou, China;College of Animal Science and Technology, Key Laboratory for Plateau Fishery Resources Conservation and Sustainable Utilization of Yunnan Province, Yunnan Agricultural University, 650201, Kunming, China;College of Fisheries, Hubei Provincial Engineering Laboratory for Pond Aquaculture, Huazhong Agricultural University, 430070, Wuhan, China;Aquaculture and Genetic Breeding Laboratory, Freshwater Fisheries Research Institute of Fujian, 350002, Fuzhou, China;College of Fisheries, Hubei Provincial Engineering Laboratory for Pond Aquaculture, Huazhong Agricultural University, 430070, Wuhan, China;Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, 430070, Wuhan, China;Department of Neurosciences and Developmental Biology, University of Vienna, 1090, Vienna, Austria;Freshwater Fisheries Research Institute of Fujian, 350002, Fuzhou, China;Fujian Key Laboratory of Developmental and Neural Biology & Southern Center for Biomedical Research, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, China;Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization, 350117, Fuzhou, Fujian, China;Institute of Oceanography, Minjiang University, 350108, Fuzhou, China;

关键词: Heterochromatin;    Centromere;    Sex chromosome;    Fish genome;    Recombination suppression;   

DOI  :  10.1186/s13059-021-02430-y

来源: Springer

【 摘 要 】

BackgroundThe origin of sex chromosomes requires the establishment of recombination suppression between the proto-sex chromosomes. In many fish species, the sex chromosome pair is homomorphic with a recent origin, providing species for studying how and why recombination suppression evolved in the initial stages of sex chromosome differentiation, but this requires accurate sequence assembly of the X and Y (or Z and W) chromosomes, which may be difficult if they are recently diverged.ResultsHere we produce a haplotype-resolved genome assembly of zig-zag eel (Mastacembelus armatus), an aquaculture fish, at the chromosomal scale. The diploid assembly is nearly gap-free, and in most chromosomes, we resolve the centromeric and subtelomeric heterochromatic sequences. In particular, the Y chromosome, including its highly repetitive short arm, has zero gaps. Using resequencing data, we identify a ~7 Mb fully sex-linked region (SLR), spanning the sex chromosome centromere and almost entirely embedded in the pericentromeric heterochromatin. The SLRs on the X and Y chromosomes are almost identical in sequence and gene content, but both are repetitive and heterochromatic, consistent with zero or low recombination. We further identify an HMG-domain containing gene HMGN6 in the SLR as a candidate sex-determining gene that is expressed at the onset of testis development.ConclusionsOur study supports the idea that preexisting regions of low recombination, such as pericentromeric regions, can give rise to SLR in the absence of structural variations between the proto-sex chromosomes.

【 授权许可】

CC BY